Table 6. Associations of specific cmPCR amplicon sequence subtypes with pneumococci, non-pneumococcal species, or unknown species based upon culture and lytA assay findings.
| cmPCR type (total combined positive A-NP/OPs and C-NPs from study)a |
Amplicon length in bp |
cmPCR amplicon sequence subtypeb (No. sequenced) |
%amplicon sequence identity with Spn reference |
No. specimens characterized byc | Culture and/or lytA-based species associationd (Spn serotype) |
|||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cultured Spn of the corresponding serotype |
Cultured non-Spn carrying sequence | lytA+ | lytA- | Adult NP/OP |
Child NP |
|||||
| 1 (14) | 214 | st1.1 (3) | 100 | 1 | 0 | 3 | 0 | 2 | 1 | S. pneumoniae (1) |
| 2 (56) | 230 | 378.2 (2) | 97.8 | 0 | 0 | 1 | 1 | 2 | 0 | non-Spn |
| 291.2 (1) | 97.4 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 300.2 (1) | 97.0 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 327.2 (1) | 97.8 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 3 (16) | 309 | 41.3 (7) | 98.7 | 2 | 0 | 7 | 0 | 3 | 4 | Spn (3) |
| st3.3 (1) | 100 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 4 (18) | 368 | st4.4 (5) | 100 | 1 | 0 | 5 | 0 | 3 | 2 | Spn (4) |
| 394.4 (3) | 94.6 | 0 | 0 | 2 | 1 | 3 | 0 | non-Spn | ||
| 5 (53) | 295 | 361.5 (6) | 98.6 | 0 | 0 | 5 | 1 | 6 | 0 | non-Spn |
| st5.5 (3) | 100 | 2 | 0 | 3 | 0 | 0 | 3 | Spn (5) | ||
| 294.5 (1) | 96.6 | 0 | 1 | 1 | 0 | 1 | 0 | S. mitis | ||
| 90.5 (1) | 96.9 | 0 | 0 | 1 | 0 | 0 | 1 | unknown | ||
| 283.5 (1) | 96.3 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 300.5 (1) | 99.0 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 392.5 (1) | 99.3 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 6AB (50) | 191 | 141.6 (6) | 97.9 | 0 | 0 | 6 | 0 | 0 | 6 | unknown |
| st6A.6 (7) | 100 | 1 | 0 | 7 | 0 | 1 | 6 | Spn (6A) | ||
| 359.6 (2) | 99.0 | 1 | 0 | 2 | 0 | 2 | 0 | Spn (6B) | ||
| 267.6 (1) | 99.5 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 7FA (25) | 546 | 254.7 (2) | 97.1 | 0 | 0 | 1 | 1 | 2 | 0 | non-Spn |
| 274.7 (1) | 97.8 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 377.7 (1) | 98.2 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 398.7 (1) | 98.4 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| st7F.7 (1) | 100 | 1 | 0 | 1 | 0 | 1 | 0 | Spn (7F) | ||
| 9NL (26) | 464 | 119.9 (1) | 99.4 | 1 | 0 | 1 | 0 | 0 | 1 | Spn (9L) |
| 300.9 (1) | 97.8 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 9VA (3) | 759 | st9V.9 (1) | 100 | 1 | 0 | 1 | 0 | 0 | 1 | Spn (9V) |
| 10A (42) | 567 | 47.10A (1) | 99.8 | 1 | 0 | 1 | 0 | 0 | 1 | Spn (10A) |
| 300.10A (1) | 96.1 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 10F/10C/33C (140) | 192 | 49.10 (2) | 92.7 | 0 | 0 | 1 | 1 | 1 | 1 | non-Spn |
| 32.10 (1) | 92.7 | 0 | 2d | 0 | 1 | 0 | 1 | non-Spn | ||
| 300.10 (1) | 92.7 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| st10F.10 (1) | 100 | 1 | 0 | 1 | 0 | 0 | 1 | Spn (10F) | ||
| 248.10 (1) | 93.2 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 265.10 (1) | 92.7 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| 378.10 (2) | 91.7 | 0 | 2 | 1 | 2 | 2 | 0 | S. oralis | ||
| 387.10(1) | 93.8 | 0 | 1 | 0 | 1 | 1 | 0 | S. parasanguinis | ||
| 12FAB/44/46 (30) | 321 | 376.12(1) | 99.7 | 0 | 1 | 0 | 1 | 1 | 0 | S. oralis |
| 13 (22) | 596 | 375.13 (1) | 83.6 | 0 | 1 | 0 | 1 | 1 | 0 | S. oralis |
| 321.13 (1) | 99.5 | 1 | 0 | 1 | 0 | 1 | 0 | Spn (13) | ||
| 14 (32) | 130 | st14.14 (11) | 100 | 1 | 0 | 11 | 0 | 3 | 8 | Spn (14) |
| 15AF (12) | 362 | 276.15 (1) | 87.8 | 0 | 1 | 0 | 1 | 1 | 0 | S. oralis |
| 17F (34) | 628 | st17F.17F(1) | 100 | 1 | 0 | 1 | 0 | 0 | 1 | Spn (17F) |
| 300.17F (1) | 91.4 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 18CABF (102) | 511 | 257.18 (2) | 90.4 | 0 | 1 | 1 | 1 | 1 | 1 | S. mitis |
| 269.18 (4) | 92.5 | 0 | 0 | 2 | 2 | 4 | 0 | non-Spn | ||
| 368 (1) | 91.1 | 0 | 0 | 1 | 0 | 1 | 0 | unknown | ||
| st18A.18 (6) | 100 | 4 | 0 | 6 | 0 | 1 | 5 | Spn (18A) | ||
| st18C.18 (4) | 100 | 3 | 0 | 4 | 0 | 2 | 2 | Spn (18C) | ||
| 19A (8) | 511 | st19A.19A(3) | 100 | 1 | 0 | 3 | 0 | 0 | 3 | Spn (19A) |
| 19F (51) | 241 | st19F.19F(9) | 100 | 1 | 0 | 9 | 0 | 3 | 6 | Spn (19F) |
| 22F/22A (32) | 579 | 276.22 (3) | 95.7 | 0 | 0 | 2 | 1 | 3 | 0 | non-Spn |
| 395.22 (2) | 94.3 | 0 | 0 | 2 | 0 | 2 | 0 | unknown | ||
| 344.22 (1) | 95.9 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 23F (38) | 319 | st23F.23F(11) | 100 | 1 | 0 | 11 | 0 | 2 | 9 | Spn (23F) |
| 33F/33A/37 (87) | 280 | 329.33 (3) | 96.4 | 0 | 0 | 2 | 1 | 3 | 0 | non-Spn |
| 383.33 (2) | 98.2 | 0 | 0 | 2 | 0 | 2 | 0 | unknown | ||
| 291.33 (1) | 96.8 | 0 | 1 | 1 | 0 | 1 | 0 | S. oralis | ||
| 344.33 (1) | 97.9 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn | ||
| 39 (53) | 38 | st39.39 (1) | 100 | 0 | 0 | 0 | 1 | 1 | 0 | non-Spn |
Notes.
a
Derived from adding positive cmPCR specimens from the 395 total specimens listed in column 3 of Tables 2–4.
b
Subtype designations start with “st” for sequences that share complete identity to the corresponding pneumococcal reference (for listing of GenBank accessions and coordinates, see http://www.cdc.gov/ncidod/biotech/files/pcr-oligonucleotide-primers.pdf).
c
Gray shaded boxes indicate data associating cmPCR sequence subtypes with pneumococcal or non-pneumococcal sources.
d
Although not found in these study isolates, was previously observed within 2 independent laboratory reference strains of S. oralis (Bishop et al., 2009).